23 papers · ranked by Valyu relevance
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 5 more
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 6 more
'Julia Mai' 'Ruth Verstraten' 'Sabrina Schreiner' 'Angus C. Wilson' 'Daniel P. Depledge' 'Evelien M. Adriaenssens'] Title: ABSTRACT Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to…
Jorge L. Pérez-Moreno, Mihika T. Kozma, Danielle M. DeLeo, Heather D. Bracken-Grissom + 2 more
Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption…
Parul Tyagi, Deeksha Singh, Shivangi Mathur, Ayushi Singh + 1 more
'Rajiv Ranjan'] Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and…
Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng + 1 more
'Tomáš Pluskal'] Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore…
Alexandra Lee, Taylor Reiter, Georgia Doing, Julia Oh + 2 more
'Deborah A. Hogan' 'Casey S. Greene'] A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems…
Kevin Vo, Ryan Mohamadi, Yashica Sharma, Amelia Mohamadi + 2 more
RNA sequencing (RNA-Seq) has become a widely adopted genome-wide technique for investigating gene expression patterns. However, conventional RNA-Seq analyses typically rely on gene expression (GE) values that aggregate all the transcripts produced by a gene under a single identifier, overlooking the complexity of…
Nurul Arneida Husin
Durio zibethinus is a popular seasonal fruit among the Asian population and is frequently associated with economic losses due to a rapid post-harvest process. To identify novel transcripts and characterize D. zibethinus transcriptome, we employed high throughput RNA-Seq analysis. In this study, we characterized the…
Roderic Guigó
Title: Summary Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of…
Hyeongseon Jeon, Juan Xie, Yeseul Jeon, Kyeong Joo Jung + 3 more
'Arkobrato Gupta' 'Won Chang' 'Dongjun Chung'] Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct…
Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, Dana Wyman + 41 more
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3’ end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much…
Hao Yuan, Christopher A Mancuso, Kayla A Johnson, Ingo Braasch + 1 more
'Arjun Krishnan'] - Hao Yuan 0000-0002-8848-1595 · yhadevol · yhbioinfo Genetics and Genome Science Program; Ecology, Evolution, and Behavior Program, Michigan State University - Christopher A. Mancuso 0000-0003-3081-2758 · ChristopherMancuso · ChrisAMancuso Department of Biostatistics & Informatics, University of…
Arnaud N’Guessan, Wen Yuan Tong, Hamed Heydari, Alex N Nguyen Ba
Genotype-phenotype mapping (GPM), or the association of trait variation to genetic variation, has been a long-lasting problem in biology. The existing approaches to this problem allowed researchers to partially understand within– and between-species variation as well as the emergence or evolution of phenotypes.…
Carolina Monzó, Adam Frankish, Ana Conesa
Long-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated genomes, while developing new algorithms and…
Wend Yam D D Ouedraogo, Aida Ouangraoua
Eukaryotic genes can encode multiple distinct transcripts through the alternative splicing (AS) of genes. Interest in the AS mechanism and its evolution across different species has stimulated numerous studies, leading to several databases that provide information on AS and transcriptome data across multiple eukaryotic…
Marjan Hosseini, Devin McConnell, Derek Aguiar
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer full-length transcripts from high-throughput sequencing data. However, this is a…
Anna Kozlova, Elizaveta Sarygina, Ekaterina Ilgisonis, Svetlana Tarbeeva + 1 more
'Svetlana Tarbeeva' 'Elena Ponomarenko'] Gene expression is a tightly regulated process that involves multiple layers of control, including transcriptional, post-transcriptional, and translational regulation. To gain a comprehensive understanding of gene expression dynamics and its functional implications, it is…
Paulo Amaral, Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial + 17 more
'Tiago Faial' 'Adam Frankish' 'T Gingeras' 'Roderic Guigó' 'Jennifer Harrow' 'Artemis G. Hatzigeorgiou' 'Rory Johnson' 'Terence D. Murphy' 'Mihaela Pertea' 'Kim D. Pruitt' 'Shashikant Pujar' 'Hazuki Takahashi' 'Igor Ulitsky' 'Ales Varabyou' 'Christine A. Wells' 'Mark Yandell' 'Piero Carninci' 'Steven L. Salzberg']…
N. Ogata, Aoi Hosaka
—Many studies used the Shannon entropy of transcriptome data to determine cell dedifferentiation and differentiation. The collection of evidence has strengthened the certainty that the transcriptome's Shannon entropy may be used to quantify cellular dedifferentiation and differentiation. Quantifying this cellular…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…